Goal: Do an MDS plot using Irene’s SNPs to look for relatedness among plants

Snp calling with freebayes

First, need to call SNPs using all BAM files at once:

working in directory 2019/IreneSnps on whitney

first, sort bams

for f in SNPanalysis/*LT*rmdup.bam
    do 
       newname=`basename $f .bam`_sort.bam
       samtools sort -o $newname --reference SNPanalysis/Pinsaporeference1 $f 
    done

next, assign read groups to bams

input=""

for f in `ls *sort.bam`
   do
      rg=`basename $f _rmdup_sort.bam`
      input="$input -b $f -r $rg -s $rg"
  done

echo $input

bamaddrg $input > LT_rmdup_sort_combined.bam

samtools index LT_rmdup_sort_combined.bam
freebayes -f SNPanalysis/Pinsaporeference1 --no-indels --no-mnps --no-complex LT_rmdup_sort_combined.bam > LT.vcf &

try parallel

ulimit -n 4000
/usr/local/stow/freebayes/scripts/fasta_generate_regions.py Pinsaporeference1.fai 100000 > regions
./freebayes-parallel regions 8 -f Pinsaporeference1 --no-indels --no-mnps --no-complex LT_rmdup_sort_combined.bam > LT.vcf 

(note: I edited the freebayes-parallel script so that it would work…)

Freeybayes parallel takes about 12 hours

scp whitney.plb.ucdavis.edu:2019/IreneSnps/LT.vcf.gz ../input/

now analyze vcf in R

library(tidyverse)

get the vcf header

vcf.header <- system("zgrep '#C' ../input/LT.vcf.gz",intern = TRUE) 
vcf.header
[1] "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t38LTR\t42LTR\t42LTRR\t43LTR\t43LTRR\t49LTWR\t49LTWRR\t95LTWR\t95LTWRR\t99LTWR"
vcf.header <- vcf.header %>% 
  str_replace("#","") %>% #get rid of the pound sign
  str_split(pattern = "\t") %>% #split on the tabs
  magrittr::extract2(1)
vcf.header
 [1] "CHROM"   "POS"     "ID"      "REF"     "ALT"     "QUAL"    "FILTER"  "INFO"    "FORMAT"  "38LTR"   "42LTR"   "42LTRR"  "43LTR"   "43LTRR"  "49LTWR"  "49LTWRR"
[17] "95LTWR"  "95LTWRR" "99LTWR" 

get the data

snps <- read_tsv("../input/LT.vcf.gz", na = c("","NA","."),comment="#",col_names = vcf.header) %>%
  select(-ID, -FILTER) # these are empty columns
Parsed with column specification:
cols(
  CHROM = col_character(),
  POS = col_integer(),
  ID = col_character(),
  REF = col_character(),
  ALT = col_character(),
  QUAL = col_double(),
  FILTER = col_character(),
  INFO = col_character(),
  FORMAT = col_character(),
  `38LTR` = col_character(),
  `42LTR` = col_character(),
  `42LTRR` = col_character(),
  `43LTR` = col_character(),
  `43LTRR` = col_character(),
  `49LTWR` = col_character(),
  `49LTWRR` = col_character(),
  `95LTWR` = col_character(),
  `95LTWRR` = col_character(),
  `99LTWR` = col_character()
)

|=================                                                                                                                                        |  11%   44 MB
|=================                                                                                                                                        |  11%   44 MB
|=================                                                                                                                                        |  11%   44 MB
|=================                                                                                                                                        |  11%   45 MB
|=================                                                                                                                                        |  11%   45 MB
|=================                                                                                                                                        |  11%   46 MB
|=================                                                                                                                                        |  11%   46 MB
|==================                                                                                                                                       |  11%   46 MB
|==================                                                                                                                                       |  11%   47 MB
|==================                                                                                                                                       |  11%   47 MB
|==================                                                                                                                                       |  12%   47 MB
|==================                                                                                                                                       |  12%   48 MB
|==================                                                                                                                                       |  12%   48 MB
|==================                                                                                                                                       |  12%   49 MB
|===================                                                                                                                                      |  12%   49 MB
|===================                                                                                                                                      |  12%   49 MB
|===================                                                                                                                                      |  12%   50 MB
|===================                                                                                                                                      |  12%   50 MB
|===================                                                                                                                                      |  12%   51 MB
|===================                                                                                                                                      |  12%   51 MB
|====================                                                                                                                                     |  12%   51 MB
|====================                                                                                                                                     |  13%   52 MB
|====================                                                                                                                                     |  13%   52 MB
|====================                                                                                                                                     |  13%   53 MB
|====================                                                                                                                                     |  13%   53 MB
|====================                                                                                                                                     |  13%   53 MB
|====================                                                                                                                                     |  13%   54 MB
|=====================                                                                                                                                    |  13%   54 MB
|=====================                                                                                                                                    |  13%   54 MB
|=====================                                                                                                                                    |  13%   55 MB
|=====================                                                                                                                                    |  13%   55 MB
|=====================                                                                                                                                    |  14%   56 MB
|=====================                                                                                                                                    |  14%   56 MB
|=====================                                                                                                                                    |  14%   56 MB
|======================                                                                                                                                   |  14%   57 MB
|======================                                                                                                                                   |  14%   57 MB
|======================                                                                                                                                   |  14%   57 MB
|======================                                                                                                                                   |  14%   58 MB
|======================                                                                                                                                   |  14%   58 MB
|======================                                                                                                                                   |  14%   59 MB
|======================                                                                                                                                   |  14%   59 MB
|=======================                                                                                                                                  |  15%   59 MB
|=======================                                                                                                                                  |  15%   60 MB
|=======================                                                                                                                                  |  15%   60 MB
|=======================                                                                                                                                  |  15%   61 MB
|=======================                                                                                                                                  |  15%   61 MB
|=======================                                                                                                                                  |  15%   61 MB
|========================                                                                                                                                 |  15%   62 MB
|========================                                                                                                                                 |  15%   62 MB
|========================                                                                                                                                 |  15%   63 MB
|========================                                                                                                                                 |  15%   63 MB
|========================                                                                                                                                 |  15%   63 MB
|========================                                                                                                                                 |  16%   64 MB
|========================                                                                                                                                 |  16%   64 MB
|=========================                                                                                                                                |  16%   64 MB
|=========================                                                                                                                                |  16%   65 MB
|=========================                                                                                                                                |  16%   65 MB
|=========================                                                                                                                                |  16%   66 MB
|=========================                                                                                                                                |  16%   66 MB
|=========================                                                                                                                                |  16%   66 MB
|=========================                                                                                                                                |  16%   67 MB
|==========================                                                                                                                               |  16%   67 MB
|==========================                                                                                                                               |  17%   68 MB
|==========================                                                                                                                               |  17%   68 MB
|==========================                                                                                                                               |  17%   68 MB
|==========================                                                                                                                               |  17%   69 MB
|==========================                                                                                                                               |  17%   69 MB
|===========================                                                                                                                              |  17%   69 MB
|===========================                                                                                                                              |  17%   70 MB
|===========================                                                                                                                              |  17%   70 MB
|===========================                                                                                                                              |  17%   71 MB
|===========================                                                                                                                              |  17%   71 MB
|===========================                                                                                                                              |  18%   71 MB
|===========================                                                                                                                              |  18%   72 MB
|============================                                                                                                                             |  18%   72 MB
|============================                                                                                                                             |  18%   73 MB
|============================                                                                                                                             |  18%   73 MB
|============================                                                                                                                             |  18%   73 MB
|============================                                                                                                                             |  18%   74 MB
|============================                                                                                                                             |  18%   74 MB
|============================                                                                                                                             |  18%   74 MB
|=============================                                                                                                                            |  18%   75 MB
|=============================                                                                                                                            |  18%   75 MB
|=============================                                                                                                                            |  19%   76 MB
|=============================                                                                                                                            |  19%   76 MB
|=============================                                                                                                                            |  19%   76 MB
|=============================                                                                                                                            |  19%   77 MB
|=============================                                                                                                                            |  19%   77 MB
|==============================                                                                                                                           |  19%   78 MB
|==============================                                                                                                                           |  19%   78 MB
|==============================                                                                                                                           |  19%   78 MB
|==============================                                                                                                                           |  19%   79 MB
|==============================                                                                                                                           |  19%   79 MB
|==============================                                                                                                                           |  20%   79 MB
|===============================                                                                                                                          |  20%   80 MB
|===============================                                                                                                                          |  20%   80 MB
|===============================                                                                                                                          |  20%   81 MB
|===============================                                                                                                                          |  20%   81 MB
|===============================                                                                                                                          |  20%   81 MB
|===============================                                                                                                                          |  20%   82 MB
|===============================                                                                                                                          |  20%   82 MB
|================================                                                                                                                         |  20%   83 MB
|================================                                                                                                                         |  20%   83 MB
|================================                                                                                                                         |  21%   83 MB
|================================                                                                                                                         |  21%   84 MB
|================================                                                                                                                         |  21%   84 MB
|================================                                                                                                                         |  21%   84 MB
|================================                                                                                                                         |  21%   85 MB
|=================================                                                                                                                        |  21%   85 MB
|=================================                                                                                                                        |  21%   86 MB
|=================================                                                                                                                        |  21%   86 MB
|=================================                                                                                                                        |  21%   86 MB
|=================================                                                                                                                        |  21%   87 MB
|=================================                                                                                                                        |  21%   87 MB
|=================================                                                                                                                        |  22%   87 MB
|==================================                                                                                                                       |  22%   88 MB
|==================================                                                                                                                       |  22%   88 MB
|==================================                                                                                                                       |  22%   89 MB
|==================================                                                                                                                       |  22%   89 MB
|==================================                                                                                                                       |  22%   89 MB
|==================================                                                                                                                       |  22%   90 MB
|==================================                                                                                                                       |  22%   90 MB
|===================================                                                                                                                      |  22%   91 MB
|===================================                                                                                                                      |  22%   91 MB
|===================================                                                                                                                      |  23%   91 MB
|===================================                                                                                                                      |  23%   92 MB
|===================================                                                                                                                      |  23%   92 MB
|===================================                                                                                                                      |  23%   92 MB
|====================================                                                                                                                     |  23%   93 MB
|====================================                                                                                                                     |  23%   93 MB
|====================================                                                                                                                     |  23%   94 MB
|====================================                                                                                                                     |  23%   94 MB
|====================================                                                                                                                     |  23%   94 MB
|====================================                                                                                                                     |  23%   95 MB
|====================================                                                                                                                     |  23%   95 MB
|=====================================                                                                                                                    |  24%   95 MB
|=====================================                                                                                                                    |  24%   96 MB
|=====================================                                                                                                                    |  24%   96 MB
|=====================================                                                                                                                    |  24%   97 MB
|=====================================                                                                                                                    |  24%   97 MB
|=====================================                                                                                                                    |  24%   97 MB
|=====================================                                                                                                                    |  24%   98 MB
|======================================                                                                                                                   |  24%   98 MB
|======================================                                                                                                                   |  24%   99 MB
|======================================                                                                                                                   |  24%   99 MB
|======================================                                                                                                                   |  25%   99 MB
|======================================                                                                                                                   |  25%  100 MB
|======================================                                                                                                                   |  25%  100 MB
|======================================                                                                                                                   |  25%  100 MB
|=======================================                                                                                                                  |  25%  101 MB
|=======================================                                                                                                                  |  25%  101 MB
|=======================================                                                                                                                  |  25%  102 MB
|=======================================                                                                                                                  |  25%  102 MB
|=======================================                                                                                                                  |  25%  102 MB
|=======================================                                                                                                                  |  25%  103 MB
|========================================                                                                                                                 |  25%  103 MB
|========================================                                                                                                                 |  26%  104 MB
|========================================                                                                                                                 |  26%  104 MB
|========================================                                                                                                                 |  26%  104 MB
|========================================                                                                                                                 |  26%  105 MB
|========================================                                                                                                                 |  26%  105 MB
|========================================                                                                                                                 |  26%  105 MB
|=========================================                                                                                                                |  26%  106 MB
|=========================================                                                                                                                |  26%  106 MB
|=========================================                                                                                                                |  26%  107 MB
|=========================================                                                                                                                |  26%  107 MB
|=========================================                                                                                                                |  27%  107 MB
|=========================================                                                                                                                |  27%  108 MB
|=========================================                                                                                                                |  27%  108 MB
|==========================================                                                                                                               |  27%  109 MB
|==========================================                                                                                                               |  27%  109 MB
|==========================================                                                                                                               |  27%  109 MB
|==========================================                                                                                                               |  27%  110 MB
|==========================================                                                                                                               |  27%  110 MB
|==========================================                                                                                                               |  27%  110 MB
|==========================================                                                                                                               |  27%  111 MB
|===========================================                                                                                                              |  27%  111 MB
|===========================================                                                                                                              |  28%  112 MB
|===========================================                                                                                                              |  28%  112 MB
|===========================================                                                                                                              |  28%  112 MB
|===========================================                                                                                                              |  28%  113 MB
|===========================================                                                                                                              |  28%  113 MB
|============================================                                                                                                             |  28%  114 MB
|============================================                                                                                                             |  28%  114 MB
|============================================                                                                                                             |  28%  114 MB
|============================================                                                                                                             |  28%  115 MB
|============================================                                                                                                             |  28%  115 MB
|============================================                                                                                                             |  29%  116 MB
|============================================                                                                                                             |  29%  116 MB
|=============================================                                                                                                            |  29%  116 MB
|=============================================                                                                                                            |  29%  117 MB
|=============================================                                                                                                            |  29%  117 MB
|=============================================                                                                                                            |  29%  117 MB
|=============================================                                                                                                            |  29%  118 MB
|=============================================                                                                                                            |  29%  118 MB
|=============================================                                                                                                            |  29%  119 MB
|==============================================                                                                                                           |  29%  119 MB
|==============================================                                                                                                           |  30%  119 MB
|==============================================                                                                                                           |  30%  120 MB
|==============================================                                                                                                           |  30%  120 MB
|==============================================                                                                                                           |  30%  121 MB
|==============================================                                                                                                           |  30%  121 MB
|===============================================                                                                                                          |  30%  121 MB
|===============================================                                                                                                          |  30%  122 MB
|===============================================                                                                                                          |  30%  122 MB
|===============================================                                                                                                          |  30%  122 MB
|===============================================                                                                                                          |  30%  123 MB
|===============================================                                                                                                          |  31%  123 MB
|===============================================                                                                                                          |  31%  124 MB
|================================================                                                                                                         |  31%  124 MB
|================================================                                                                                                         |  31%  124 MB
|================================================                                                                                                         |  31%  125 MB
|================================================                                                                                                         |  31%  125 MB
|================================================                                                                                                         |  31%  126 MB
|================================================                                                                                                         |  31%  126 MB
|================================================                                                                                                         |  31%  126 MB
|=================================================                                                                                                        |  31%  127 MB
|=================================================                                                                                                        |  31%  127 MB
|=================================================                                                                                                        |  32%  128 MB
|=================================================                                                                                                        |  32%  128 MB
|=================================================                                                                                                        |  32%  128 MB
|=================================================                                                                                                        |  32%  129 MB
|==================================================                                                                                                       |  32%  129 MB
|==================================================                                                                                                       |  32%  129 MB
|==================================================                                                                                                       |  32%  130 MB
|==================================================                                                                                                       |  32%  130 MB
|==================================================                                                                                                       |  32%  131 MB
|==================================================                                                                                                       |  32%  131 MB
|==================================================                                                                                                       |  33%  131 MB
|===================================================                                                                                                      |  33%  132 MB
|===================================================                                                                                                      |  33%  132 MB
|===================================================                                                                                                      |  33%  133 MB
|===================================================                                                                                                      |  33%  133 MB
|===================================================                                                                                                      |  33%  133 MB
|===================================================                                                                                                      |  33%  134 MB
|====================================================                                                                                                     |  33%  134 MB
|====================================================                                                                                                     |  33%  135 MB
|====================================================                                                                                                     |  33%  135 MB
|====================================================                                                                                                     |  34%  135 MB
|====================================================                                                                                                     |  34%  136 MB
|====================================================                                                                                                     |  34%  136 MB
|====================================================                                                                                                     |  34%  137 MB
|=====================================================                                                                                                    |  34%  137 MB
|=====================================================                                                                                                    |  34%  137 MB
|=====================================================                                                                                                    |  34%  138 MB
|=====================================================                                                                                                    |  34%  138 MB
|=====================================================                                                                                                    |  34%  139 MB
|=====================================================                                                                                                    |  34%  139 MB
|=====================================================                                                                                                    |  35%  139 MB
|======================================================                                                                                                   |  35%  140 MB
|======================================================                                                                                                   |  35%  140 MB
|======================================================                                                                                                   |  35%  141 MB
|======================================================                                                                                                   |  35%  141 MB
|======================================================                                                                                                   |  35%  141 MB
|======================================================                                                                                                   |  35%  142 MB
|=======================================================                                                                                                  |  35%  142 MB
|=======================================================                                                                                                  |  35%  142 MB
|=======================================================                                                                                                  |  35%  143 MB
|=======================================================                                                                                                  |  36%  143 MB
|=======================================================                                                                                                  |  36%  144 MB
|=======================================================                                                                                                  |  36%  144 MB
|=======================================================                                                                                                  |  36%  144 MB
|========================================================                                                                                                 |  36%  145 MB
|========================================================                                                                                                 |  36%  145 MB
|========================================================                                                                                                 |  36%  146 MB
|========================================================                                                                                                 |  36%  146 MB
|========================================================                                                                                                 |  36%  146 MB
|========================================================                                                                                                 |  36%  147 MB
|========================================================                                                                                                 |  37%  147 MB
|=========================================================                                                                                                |  37%  148 MB
|=========================================================                                                                                                |  37%  148 MB
|=========================================================                                                                                                |  37%  148 MB
|=========================================================                                                                                                |  37%  149 MB
|=========================================================                                                                                                |  37%  149 MB
|=========================================================                                                                                                |  37%  150 MB
|==========================================================                                                                                               |  37%  150 MB
|==========================================================                                                                                               |  37%  150 MB
|==========================================================                                                                                               |  37%  151 MB
|==========================================================                                                                                               |  37%  151 MB
|==========================================================                                                                                               |  38%  151 MB
|==========================================================                                                                                               |  38%  152 MB
|==========================================================                                                                                               |  38%  152 MB
|===========================================================                                                                                              |  38%  153 MB
|===========================================================                                                                                              |  38%  153 MB
|===========================================================                                                                                              |  38%  153 MB
|===========================================================                                                                                              |  38%  154 MB
|===========================================================                                                                                              |  38%  154 MB
|===========================================================                                                                                              |  38%  155 MB
|============================================================                                                                                             |  38%  155 MB
|============================================================                                                                                             |  39%  155 MB
|============================================================                                                                                             |  39%  156 MB
|============================================================                                                                                             |  39%  156 MB
|============================================================                                                                                             |  39%  157 MB
|============================================================                                                                                             |  39%  157 MB
|============================================================                                                                                             |  39%  157 MB
|=============================================================                                                                                            |  39%  158 MB
|=============================================================                                                                                            |  39%  158 MB
|=============================================================                                                                                            |  39%  159 MB
|=============================================================                                                                                            |  39%  159 MB
|=============================================================                                                                                            |  40%  159 MB
|=============================================================                                                                                            |  40%  160 MB
|=============================================================                                                                                            |  40%  160 MB
|==============================================================                                                                                           |  40%  160 MB
|==============================================================                                                                                           |  40%  161 MB
|==============================================================                                                                                           |  40%  161 MB
|==============================================================                                                                                           |  40%  162 MB
|==============================================================                                                                                           |  40%  162 MB
|==============================================================                                                                                           |  40%  162 MB
|===============================================================                                                                                          |  40%  163 MB
|===============================================================                                                                                          |  41%  163 MB
|===============================================================                                                                                          |  41%  164 MB
|===============================================================                                                                                          |  41%  164 MB
|===============================================================                                                                                          |  41%  164 MB
|===============================================================                                                                                          |  41%  165 MB
|===============================================================                                                                                          |  41%  165 MB
|================================================================                                                                                         |  41%  166 MB
|================================================================                                                                                         |  41%  166 MB
|================================================================                                                                                         |  41%  166 MB
|================================================================                                                                                         |  41%  167 MB
|================================================================                                                                                         |  42%  167 MB
|================================================================                                                                                         |  42%  168 MB
|=================================================================                                                                                        |  42%  168 MB
|=================================================================                                                                                        |  42%  168 MB
|=================================================================                                                                                        |  42%  169 MB
|=================================================================                                                                                        |  42%  169 MB
|=================================================================                                                                                        |  42%  170 MB
|=================================================================                                                                                        |  42%  170 MB
|==================================================================                                                                                       |  42%  171 MB
|==================================================================                                                                                       |  42%  171 MB
|==================================================================                                                                                       |  43%  171 MB
|==================================================================                                                                                       |  43%  172 MB
|==================================================================                                                                                       |  43%  172 MB
|==================================================================                                                                                       |  43%  173 MB
|==================================================================                                                                                       |  43%  173 MB
|===================================================================                                                                                      |  43%  173 MB
|===================================================================                                                                                      |  43%  174 MB
|===================================================================                                                                                      |  43%  174 MB
|===================================================================                                                                                      |  43%  175 MB
|===================================================================                                                                                      |  44%  175 MB
|===================================================================                                                                                      |  44%  175 MB
|====================================================================                                                                                     |  44%  176 MB
|====================================================================                                                                                     |  44%  176 MB
|====================================================================                                                                                     |  44%  177 MB
|====================================================================                                                                                     |  44%  177 MB
|====================================================================                                                                                     |  44%  177 MB
|====================================================================                                                                                     |  44%  178 MB
|====================================================================                                                                                     |  44%  178 MB
|=====================================================================                                                                                    |  44%  179 MB
|=====================================================================                                                                                    |  44%  179 MB
|=====================================================================                                                                                    |  45%  179 MB
|=====================================================================                                                                                    |  45%  180 MB
|=====================================================================                                                                                    |  45%  180 MB
|=====================================================================                                                                                    |  45%  181 MB
|======================================================================                                                                                   |  45%  181 MB
|======================================================================                                                                                   |  45%  181 MB
|======================================================================                                                                                   |  45%  182 MB
|======================================================================                                                                                   |  45%  182 MB
|======================================================================                                                                                   |  45%  183 MB
|======================================================================                                                                                   |  46%  183 MB
|======================================================================                                                                                   |  46%  183 MB
|=======================================================================                                                                                  |  46%  184 MB
|=======================================================================                                                                                  |  46%  184 MB
|=======================================================================                                                                                  |  46%  185 MB
|=======================================================================                                                                                  |  46%  185 MB
|=======================================================================                                                                                  |  46%  185 MB
|=======================================================================                                                                                  |  46%  186 MB
|========================================================================                                                                                 |  46%  186 MB
|========================================================================                                                                                 |  46%  187 MB
|========================================================================                                                                                 |  46%  187 MB
|========================================================================                                                                                 |  47%  187 MB
|========================================================================                                                                                 |  47%  188 MB
|========================================================================                                                                                 |  47%  188 MB
|========================================================================                                                                                 |  47%  188 MB
|=========================================================================                                                                                |  47%  189 MB
|=========================================================================                                                                                |  47%  189 MB
|=========================================================================                                                                                |  47%  190 MB
|=========================================================================                                                                                |  47%  190 MB
|=========================================================================                                                                                |  47%  190 MB
|=========================================================================                                                                                |  47%  191 MB
|==========================================================================                                                                               |  48%  191 MB
|==========================================================================                                                                               |  48%  192 MB
|==========================================================================                                                                               |  48%  192 MB
|==========================================================================                                                                               |  48%  193 MB
|==========================================================================                                                                               |  48%  193 MB
|==========================================================================                                                                               |  48%  193 MB
|==========================================================================                                                                               |  48%  194 MB
|===========================================================================                                                                              |  48%  194 MB
|===========================================================================                                                                              |  48%  194 MB
|===========================================================================                                                                              |  48%  195 MB
|===========================================================================                                                                              |  49%  195 MB
|===========================================================================                                                                              |  49%  196 MB
|===========================================================================                                                                              |  49%  196 MB
|============================================================================                                                                             |  49%  196 MB
|============================================================================                                                                             |  49%  197 MB
|============================================================================                                                                             |  49%  197 MB
|============================================================================                                                                             |  49%  198 MB
|============================================================================                                                                             |  49%  198 MB
|============================================================================                                                                             |  49%  199 MB
|============================================================================                                                                             |  49%  199 MB
|=============================================================================                                                                            |  50%  199 MB
|=============================================================================                                                                            |  50%  200 MB
|=============================================================================                                                                            |  50%  200 MB
|=============================================================================                                                                            |  50%  201 MB
|=============================================================================                                                                            |  50%  201 MB
|=============================================================================                                                                            |  50%  201 MB
|==============================================================================                                                                           |  50%  202 MB
|==============================================================================                                                                           |  50%  202 MB
|==============================================================================                                                                           |  50%  203 MB
|==============================================================================                                                                           |  50%  203 MB
|==============================================================================                                                                           |  51%  203 MB
|==============================================================================                                                                           |  51%  204 MB
|==============================================================================                                                                           |  51%  204 MB
|===============================================================================                                                                          |  51%  204 MB
|===============================================================================                                                                          |  51%  205 MB
|===============================================================================                                                                          |  51%  205 MB
|===============================================================================                                                                          |  51%  206 MB
|===============================================================================                                                                          |  51%  206 MB
|===============================================================================                                                                          |  51%  206 MB
|================================================================================                                                                         |  51%  207 MB
|================================================================================                                                                         |  52%  207 MB
|================================================================================                                                                         |  52%  208 MB
|================================================================================                                                                         |  52%  208 MB
|================================================================================                                                                         |  52%  208 MB
|================================================================================                                                                         |  52%  209 MB
|================================================================================                                                                         |  52%  209 MB
|=================================================================================                                                                        |  52%  210 MB
|=================================================================================                                                                        |  52%  210 MB
|=================================================================================                                                                        |  52%  210 MB
|=================================================================================                                                                        |  52%  211 MB
|=================================================================================                                                                        |  53%  211 MB
|=================================================================================                                                                        |  53%  212 MB
|==================================================================================                                                                       |  53%  212 MB
|==================================================================================                                                                       |  53%  212 MB
|==================================================================================                                                                       |  53%  213 MB
|==================================================================================                                                                       |  53%  213 MB
|==================================================================================                                                                       |  53%  213 MB
|==================================================================================                                                                       |  53%  214 MB
|==================================================================================                                                                       |  53%  214 MB
|===================================================================================                                                                      |  53%  215 MB
|===================================================================================                                                                      |  54%  215 MB
|===================================================================================                                                                      |  54%  216 MB
|===================================================================================                                                                      |  54%  216 MB
|===================================================================================                                                                      |  54%  216 MB
|===================================================================================                                                                      |  54%  217 MB
|===================================================================================                                                                      |  54%  217 MB
|====================================================================================                                                                     |  54%  217 MB
|====================================================================================                                                                     |  54%  218 MB
|====================================================================================                                                                     |  54%  218 MB
|====================================================================================                                                                     |  54%  219 MB
|====================================================================================                                                                     |  55%  219 MB
|====================================================================================                                                                     |  55%  219 MB
|=====================================================================================                                                                    |  55%  220 MB
|=====================================================================================                                                                    |  55%  220 MB
|=====================================================================================                                                                    |  55%  221 MB
|=====================================================================================                                                                    |  55%  221 MB
|=====================================================================================                                                                    |  55%  221 MB
|=====================================================================================                                                                    |  55%  222 MB
|=====================================================================================                                                                    |  55%  222 MB
|======================================================================================                                                                   |  55%  223 MB
|======================================================================================                                                                   |  55%  223 MB
|======================================================================================                                                                   |  56%  223 MB
|======================================================================================                                                                   |  56%  224 MB
|======================================================================================                                                                   |  56%  224 MB
|======================================================================================                                                                   |  56%  224 MB
|======================================================================================                                                                   |  56%  225 MB
|=======================================================================================                                                                  |  56%  225 MB
|=======================================================================================                                                                  |  56%  226 MB
|=======================================================================================                                                                  |  56%  226 MB
|=======================================================================================                                                                  |  56%  226 MB
|=======================================================================================                                                                  |  56%  227 MB
|=======================================================================================                                                                  |  57%  227 MB
|========================================================================================                                                                 |  57%  228 MB
|========================================================================================                                                                 |  57%  228 MB
|========================================================================================                                                                 |  57%  228 MB
|========================================================================================                                                                 |  57%  229 MB
|========================================================================================                                                                 |  57%  229 MB
|========================================================================================                                                                 |  57%  230 MB
|========================================================================================                                                                 |  57%  230 MB
|=========================================================================================                                                                |  57%  230 MB
|=========================================================================================                                                                |  57%  231 MB
|=========================================================================================                                                                |  58%  231 MB
|=========================================================================================                                                                |  58%  232 MB
|=========================================================================================                                                                |  58%  232 MB
|=========================================================================================                                                                |  58%  232 MB
|=========================================================================================                                                                |  58%  233 MB
|==========================================================================================                                                               |  58%  233 MB
|==========================================================================================                                                               |  58%  233 MB
|==========================================================================================                                                               |  58%  234 MB
|==========================================================================================                                                               |  58%  234 MB
|==========================================================================================                                                               |  58%  235 MB
|==========================================================================================                                                               |  59%  235 MB
|===========================================================================================                                                              |  59%  235 MB
|===========================================================================================                                                              |  59%  236 MB
|===========================================================================================                                                              |  59%  236 MB
|===========================================================================================                                                              |  59%  237 MB
|===========================================================================================                                                              |  59%  237 MB
|===========================================================================================                                                              |  59%  237 MB
|===========================================================================================                                                              |  59%  238 MB
|============================================================================================                                                             |  59%  238 MB
|============================================================================================                                                             |  59%  238 MB
|============================================================================================                                                             |  59%  239 MB
|============================================================================================                                                             |  60%  239 MB
|============================================================================================                                                             |  60%  240 MB
|============================================================================================                                                             |  60%  240 MB
|============================================================================================                                                             |  60%  240 MB
|=============================================================================================                                                            |  60%  241 MB
|=============================================================================================                                                            |  60%  241 MB
|=============================================================================================                                                            |  60%  242 MB
|=============================================================================================                                                            |  60%  242 MB
|=============================================================================================                                                            |  60%  242 MB
|=============================================================================================                                                            |  60%  243 MB
|==============================================================================================                                                           |  61%  243 MB
|==============================================================================================                                                           |  61%  244 MB
|==============================================================================================                                                           |  61%  244 MB
|==============================================================================================                                                           |  61%  244 MB
|==============================================================================================                                                           |  61%  245 MB
|==============================================================================================                                                           |  61%  245 MB
|==============================================================================================                                                           |  61%  246 MB
|===============================================================================================                                                          |  61%  246 MB
|===============================================================================================                                                          |  61%  246 MB
|===============================================================================================                                                          |  61%  247 MB
|===============================================================================================                                                          |  62%  247 MB
|===============================================================================================                                                          |  62%  248 MB
|===============================================================================================                                                          |  62%  248 MB
|================================================================================================                                                         |  62%  248 MB
|================================================================================================                                                         |  62%  249 MB
|================================================================================================                                                         |  62%  249 MB
|================================================================================================                                                         |  62%  249 MB
|================================================================================================                                                         |  62%  250 MB
|================================================================================================                                                         |  62%  250 MB
|================================================================================================                                                         |  62%  251 MB
|=================================================================================================                                                        |  63%  251 MB
|=================================================================================================                                                        |  63%  251 MB
|=================================================================================================                                                        |  63%  252 MB
|=================================================================================================                                                        |  63%  252 MB
|=================================================================================================                                                        |  63%  253 MB
|=================================================================================================                                                        |  63%  253 MB
|=================================================================================================                                                        |  63%  253 MB
|==================================================================================================                                                       |  63%  254 MB
|==================================================================================================                                                       |  63%  254 MB
|==================================================================================================                                                       |  63%  255 MB
|==================================================================================================                                                       |  64%  255 MB
|==================================================================================================                                                       |  64%  255 MB
|==================================================================================================                                                       |  64%  256 MB
|===================================================================================================                                                      |  64%  256 MB
|===================================================================================================                                                      |  64%  256 MB
|===================================================================================================                                                      |  64%  257 MB
|===================================================================================================                                                      |  64%  257 MB
|===================================================================================================                                                      |  64%  258 MB
|===================================================================================================                                                      |  64%  258 MB
|===================================================================================================                                                      |  64%  258 MB
|====================================================================================================                                                     |  64%  259 MB
|====================================================================================================                                                     |  65%  259 MB
|====================================================================================================                                                     |  65%  260 MB
|====================================================================================================                                                     |  65%  260 MB
|====================================================================================================                                                     |  65%  260 MB
|====================================================================================================                                                     |  65%  261 MB
|=====================================================================================================                                                    |  65%  261 MB
|=====================================================================================================                                                    |  65%  262 MB
|=====================================================================================================                                                    |  65%  262 MB
|=====================================================================================================                                                    |  65%  262 MB
|=====================================================================================================                                                    |  65%  263 MB
|=====================================================================================================                                                    |  66%  263 MB
|=====================================================================================================                                                    |  66%  264 MB
|======================================================================================================                                                   |  66%  264 MB
|======================================================================================================                                                   |  66%  264 MB
|======================================================================================================                                                   |  66%  265 MB
|======================================================================================================                                                   |  66%  265 MB
|======================================================================================================                                                   |  66%  265 MB
|======================================================================================================                                                   |  66%  266 MB
|======================================================================================================                                                   |  66%  266 MB
|=======================================================================================================                                                  |  66%  267 MB
|=======================================================================================================                                                  |  67%  267 MB
|=======================================================================================================                                                  |  67%  267 MB
|=======================================================================================================                                                  |  67%  268 MB
|=======================================================================================================                                                  |  67%  268 MB
|=======================================================================================================                                                  |  67%  269 MB
|========================================================================================================                                                 |  67%  269 MB
|========================================================================================================                                                 |  67%  269 MB
|========================================================================================================                                                 |  67%  270 MB
|========================================================================================================                                                 |  67%  270 MB
|========================================================================================================                                                 |  67%  271 MB
|========================================================================================================                                                 |  68%  271 MB
|========================================================================================================                                                 |  68%  271 MB
|=========================================================================================================                                                |  68%  272 MB
|=========================================================================================================                                                |  68%  272 MB
|=========================================================================================================                                                |  68%  273 MB
|=========================================================================================================                                                |  68%  273 MB
|=========================================================================================================                                                |  68%  273 MB
|=========================================================================================================                                                |  68%  274 MB
|=========================================================================================================                                                |  68%  274 MB
|==========================================================================================================                                               |  68%  274 MB
|==========================================================================================================                                               |  69%  275 MB
|==========================================================================================================                                               |  69%  275 MB
|==========================================================================================================                                               |  69%  276 MB
|==========================================================================================================                                               |  69%  276 MB
|==========================================================================================================                                               |  69%  277 MB
|===========================================================================================================                                              |  69%  277 MB
|===========================================================================================================                                              |  69%  277 MB
|===========================================================================================================                                              |  69%  278 MB
|===========================================================================================================                                              |  69%  278 MB
|===========================================================================================================                                              |  69%  279 MB
|===========================================================================================================                                              |  70%  279 MB
|===========================================================================================================                                              |  70%  279 MB
|============================================================================================================                                             |  70%  280 MB
|============================================================================================================                                             |  70%  280 MB
|============================================================================================================                                             |  70%  280 MB
|============================================================================================================                                             |  70%  281 MB
|============================================================================================================                                             |  70%  281 MB
|============================================================================================================                                             |  70%  282 MB
|=============================================================================================================                                            |  70%  282 MB
|=============================================================================================================                                            |  70%  282 MB
|=============================================================================================================                                            |  71%  283 MB
|=============================================================================================================                                            |  71%  283 MB
|=============================================================================================================                                            |  71%  284 MB
|=============================================================================================================                                            |  71%  284 MB
|=============================================================================================================                                            |  71%  284 MB
|==============================================================================================================                                           |  71%  285 MB
|==============================================================================================================                                           |  71%  285 MB
|==============================================================================================================                                           |  71%  285 MB
|==============================================================================================================                                           |  71%  286 MB
|==============================================================================================================                                           |  71%  286 MB
|==============================================================================================================                                           |  71%  287 MB
|==============================================================================================================                                           |  72%  287 MB
|===============================================================================================================                                          |  72%  287 MB
|===============================================================================================================                                          |  72%  288 MB
|===============================================================================================================                                          |  72%  288 MB
|===============================================================================================================                                          |  72%  289 MB
|===============================================================================================================                                          |  72%  289 MB
|===============================================================================================================                                          |  72%  289 MB
|================================================================================================================                                         |  72%  290 MB
|================================================================================================================                                         |  72%  290 MB
|================================================================================================================                                         |  72%  290 MB
|================================================================================================================                                         |  73%  291 MB
|================================================================================================================                                         |  73%  291 MB
|================================================================================================================                                         |  73%  292 MB
|================================================================================================================                                         |  73%  292 MB
|=================================================================================================================                                        |  73%  292 MB
|=================================================================================================================                                        |  73%  293 MB
|=================================================================================================================                                        |  73%  293 MB
|=================================================================================================================                                        |  73%  294 MB
|=================================================================================================================                                        |  73%  294 MB
|=================================================================================================================                                        |  73%  294 MB
|==================================================================================================================                                       |  74%  295 MB
|==================================================================================================================                                       |  74%  295 MB
|==================================================================================================================                                       |  74%  296 MB
|==================================================================================================================                                       |  74%  296 MB
|==================================================================================================================                                       |  74%  296 MB
|==================================================================================================================                                       |  74%  297 MB
|==================================================================================================================                                       |  74%  297 MB
|===================================================================================================================                                      |  74%  298 MB
|===================================================================================================================                                      |  74%  298 MB
|===================================================================================================================                                      |  74%  298 MB
|===================================================================================================================                                      |  74%  299 MB
|===================================================================================================================                                      |  75%  299 MB
|===================================================================================================================                                      |  75%  299 MB
|===================================================================================================================                                      |  75%  300 MB
|====================================================================================================================                                     |  75%  300 MB
|====================================================================================================================                                     |  75%  301 MB
|====================================================================================================================                                     |  75%  301 MB
|====================================================================================================================                                     |  75%  301 MB
|====================================================================================================================                                     |  75%  302 MB
|====================================================================================================================                                     |  75%  302 MB
|====================================================================================================================                                     |  75%  303 MB
|=====================================================================================================================                                    |  76%  303 MB
|=====================================================================================================================                                    |  76%  303 MB
|=====================================================================================================================                                    |  76%  304 MB
|=====================================================================================================================                                    |  76%  304 MB
|=====================================================================================================================                                    |  76%  304 MB
|=====================================================================================================================                                    |  76%  305 MB
|======================================================================================================================                                   |  76%  305 MB
|======================================================================================================================                                   |  76%  306 MB
|======================================================================================================================                                   |  76%  306 MB
|======================================================================================================================                                   |  76%  306 MB
|======================================================================================================================                                   |  77%  307 MB
|======================================================================================================================                                   |  77%  307 MB
|======================================================================================================================                                   |  77%  308 MB
|=======================================================================================================================                                  |  77%  308 MB
|=======================================================================================================================                                  |  77%  308 MB
|=======================================================================================================================                                  |  77%  309 MB
|=======================================================================================================================                                  |  77%  309 MB
|=======================================================================================================================                                  |  77%  310 MB
|=======================================================================================================================                                  |  77%  310 MB
|========================================================================================================================                                 |  77%  310 MB
|========================================================================================================================                                 |  78%  311 MB
|========================================================================================================================                                 |  78%  311 MB
|========================================================================================================================                                 |  78%  312 MB
|========================================================================================================================                                 |  78%  312 MB
|========================================================================================================================                                 |  78%  312 MB
|========================================================================================================================                                 |  78%  313 MB
|=========================================================================================================================                                |  78%  313 MB
|=========================================================================================================================                                |  78%  313 MB
|=========================================================================================================================                                |  78%  314 MB
|=========================================================================================================================                                |  78%  314 MB
|=========================================================================================================================                                |  78%  315 MB
|=========================================================================================================================                                |  79%  315 MB
|=========================================================================================================================                                |  79%  315 MB
|==========================================================================================================================                               |  79%  316 MB
|==========================================================================================================================                               |  79%  316 MB
|==========================================================================================================================                               |  79%  317 MB
|==========================================================================================================================                               |  79%  317 MB
|==========================================================================================================================                               |  79%  317 MB
|==========================================================================================================================                               |  79%  318 MB
|==========================================================================================================================                               |  79%  318 MB
|===========================================================================================================================                              |  79%  319 MB
|===========================================================================================================================                              |  80%  319 MB
|===========================================================================================================================                              |  80%  319 MB
|===========================================================================================================================                              |  80%  320 MB
|===========================================================================================================================                              |  80%  320 MB
|===========================================================================================================================                              |  80%  320 MB
|============================================================================================================================                             |  80%  321 MB
|============================================================================================================================                             |  80%  321 MB
|============================================================================================================================                             |  80%  322 MB
|============================================================================================================================                             |  80%  322 MB
|============================================================================================================================                             |  80%  322 MB
|============================================================================================================================                             |  81%  323 MB
|============================================================================================================================                             |  81%  323 MB
|=============================================================================================================================                            |  81%  324 MB
|=============================================================================================================================                            |  81%  324 MB
|=============================================================================================================================                            |  81%  324 MB
|=============================================================================================================================                            |  81%  325 MB
|=============================================================================================================================                            |  81%  325 MB
|=============================================================================================================================                            |  81%  326 MB
|==============================================================================================================================                           |  81%  326 MB
|==============================================================================================================================                           |  81%  326 MB
|==============================================================================================================================                           |  82%  327 MB
|==============================================================================================================================                           |  82%  327 MB
|==============================================================================================================================                           |  82%  328 MB
|==============================================================================================================================                           |  82%  328 MB
|==============================================================================================================================                           |  82%  328 MB
|===============================================================================================================================                          |  82%  329 MB
|===============================================================================================================================                          |  82%  329 MB
|===============================================================================================================================                          |  82%  330 MB
|===============================================================================================================================                          |  82%  330 MB
|===============================================================================================================================                          |  82%  330 MB
|===============================================================================================================================                          |  83%  331 MB
|================================================================================================================================                         |  83%  331 MB
|================================================================================================================================                         |  83%  332 MB
|================================================================================================================================                         |  83%  332 MB
|================================================================================================================================                         |  83%  332 MB
|================================================================================================================================                         |  83%  333 MB
|================================================================================================================================                         |  83%  333 MB
|================================================================================================================================                         |  83%  333 MB
|=================================================================================================================================                        |  83%  334 MB
|=================================================================================================================================                        |  83%  334 MB
|=================================================================================================================================                        |  83%  335 MB
|=================================================================================================================================                        |  84%  335 MB
|=================================================================================================================================                        |  84%  335 MB
|=================================================================================================================================                        |  84%  336 MB
|=================================================================================================================================                        |  84%  336 MB
|==================================================================================================================================                       |  84%  337 MB
|==================================================================================================================================                       |  84%  337 MB
|==================================================================================================================================                       |  84%  337 MB
|==================================================================================================================================                       |  84%  338 MB
|==================================================================================================================================                       |  84%  338 MB
|==================================================================================================================================                       |  84%  339 MB
|===================================================================================================================================                      |  85%  339 MB
|===================================================================================================================================                      |  85%  339 MB
|===================================================================================================================================                      |  85%  340 MB
|===================================================================================================================================                      |  85%  340 MB
|===================================================================================================================================                      |  85%  341 MB
|===================================================================================================================================                      |  85%  341 MB
|===================================================================================================================================                      |  85%  341 MB
|====================================================================================================================================                     |  85%  342 MB
|====================================================================================================================================                     |  85%  342 MB
|====================================================================================================================================                     |  85%  343 MB
|====================================================================================================================================                     |  86%  343 MB
|====================================================================================================================================                     |  86%  343 MB
|====================================================================================================================================                     |  86%  344 MB
|=====================================================================================================================================                    |  86%  344 MB
|=====================================================================================================================================                    |  86%  345 MB
|=====================================================================================================================================                    |  86%  345 MB
|=====================================================================================================================================                    |  86%  345 MB
|=====================================================================================================================================                    |  86%  346 MB
|=====================================================================================================================================                    |  86%  346 MB
|=====================================================================================================================================                    |  86%  346 MB
|======================================================================================================================================                   |  87%  347 MB
|======================================================================================================================================                   |  87%  347 MB
|======================================================================================================================================                   |  87%  348 MB
|======================================================================================================================================                   |  87%  348 MB
|======================================================================================================================================                   |  87%  348 MB
|======================================================================================================================================                   |  87%  349 MB
|======================================================================================================================================                   |  87%  349 MB
|=======================================================================================================================================                  |  87%  349 MB
|=======================================================================================================================================                  |  87%  350 MB
|=======================================================================================================================================                  |  87%  350 MB
|=======================================================================================================================================                  |  88%  351 MB
|=======================================================================================================================================                  |  88%  351 MB
|=======================================================================================================================================                  |  88%  351 MB
|=======================================================================================================================================                  |  88%  352 MB
|========================================================================================================================================                 |  88%  352 MB
|========================================================================================================================================                 |  88%  352 MB
|========================================================================================================================================                 |  88%  353 MB
|========================================================================================================================================                 |  88%  353 MB
|========================================================================================================================================                 |  88%  354 MB
|========================================================================================================================================                 |  88%  354 MB
|========================================================================================================================================                 |  88%  354 MB
|=========================================================================================================================================                |  89%  355 MB
|=========================================================================================================================================                |  89%  355 MB
|=========================================================================================================================================                |  89%  355 MB
|=========================================================================================================================================                |  89%  356 MB
|=========================================================================================================================================                |  89%  356 MB
|=========================================================================================================================================                |  89%  357 MB
|=========================================================================================================================================                |  89%  357 MB
|==========================================================================================================================================               |  89%  357 MB
|==========================================================================================================================================               |  89%  358 MB
|==========================================================================================================================================               |  89%  358 MB
|==========================================================================================================================================               |  89%  358 MB
|==========================================================================================================================================               |  90%  359 MB
|==========================================================================================================================================               |  90%  359 MB
|==========================================================================================================================================               |  90%  359 MB
|===========================================================================================================================================              |  90%  360 MB
|===========================================================================================================================================              |  90%  360 MB
|===========================================================================================================================================              |  90%  360 MB
|===========================================================================================================================================              |  90%  361 MB
|===========================================================================================================================================              |  90%  361 MB
|===========================================================================================================================================              |  90%  362 MB
|===========================================================================================================================================              |  90%  362 MB
|============================================================================================================================================             |  90%  362 MB
|============================================================================================================================================             |  91%  363 MB
|============================================================================================================================================             |  91%  363 MB
|============================================================================================================================================             |  91%  364 MB
|============================================================================================================================================             |  91%  364 MB
|============================================================================================================================================             |  91%  364 MB
|============================================================================================================================================             |  91%  365 MB
|=============================================================================================================================================            |  91%  365 MB
|=============================================================================================================================================            |  91%  366 MB
|=============================================================================================================================================            |  91%  366 MB
|=============================================================================================================================================            |  91%  366 MB
|=============================================================================================================================================            |  92%  367 MB
|=============================================================================================================================================            |  92%  367 MB
|==============================================================================================================================================           |  92%  367 MB
|==============================================================================================================================================           |  92%  368 MB
|==============================================================================================================================================           |  92%  368 MB
|==============================================================================================================================================           |  92%  369 MB
|==============================================================================================================================================           |  92%  369 MB
|==============================================================================================================================================           |  92%  369 MB
|==============================================================================================================================================           |  92%  370 MB
|===============================================================================================================================================          |  92%  370 MB
|===============================================================================================================================================          |  92%  370 MB
|===============================================================================================================================================          |  93%  371 MB
|===============================================================================================================================================          |  93%  371 MB
|===============================================================================================================================================          |  93%  372 MB
|===============================================================================================================================================          |  93%  372 MB
|===============================================================================================================================================          |  93%  372 MB
|================================================================================================================================================         |  93%  373 MB
|================================================================================================================================================         |  93%  373 MB
|================================================================================================================================================         |  93%  373 MB
|================================================================================================================================================         |  93%  374 MB
|================================================================================================================================================         |  93%  374 MB
|================================================================================================================================================         |  93%  374 MB
|================================================================================================================================================         |  94%  375 MB
|================================================================================================================================================         |  94%  375 MB
|=================================================================================================================================================        |  94%  375 MB
|=================================================================================================================================================        |  94%  376 MB
|=================================================================================================================================================        |  94%  376 MB
|=================================================================================================================================================        |  94%  377 MB
|=================================================================================================================================================        |  94%  377 MB
|=================================================================================================================================================        |  94%  377 MB
|=================================================================================================================================================        |  94%  378 MB
|==================================================================================================================================================       |  94%  378 MB
|==================================================================================================================================================       |  94%  378 MB
|==================================================================================================================================================       |  95%  379 MB
|==================================================================================================================================================       |  95%  379 MB
|==================================================================================================================================================       |  95%  379 MB
|==================================================================================================================================================       |  95%  380 MB
|==================================================================================================================================================       |  95%  380 MB
|===================================================================================================================================================      |  95%  380 MB
|===================================================================================================================================================      |  95%  381 MB
|===================================================================================================================================================      |  95%  381 MB
|===================================================================================================================================================      |  95%  382 MB
|===================================================================================================================================================      |  95%  382 MB
|===================================================================================================================================================      |  95%  382 MB
|===================================================================================================================================================      |  95%  383 MB
|===================================================================================================================================================      |  96%  383 MB
|====================================================================================================================================================     |  96%  383 MB
|====================================================================================================================================================     |  96%  384 MB
|====================================================================================================================================================     |  96%  384 MB
|====================================================================================================================================================     |  96%  384 MB
|====================================================================================================================================================     |  96%  385 MB
|====================================================================================================================================================     |  96%  385 MB
|====================================================================================================================================================     |  96%  385 MB
|=====================================================================================================================================================    |  96%  386 MB
|=====================================================================================================================================================    |  96%  386 MB
|=====================================================================================================================================================    |  96%  386 MB
|=====================================================================================================================================================    |  97%  387 MB
|=====================================================================================================================================================    |  97%  387 MB
|=====================================================================================================================================================    |  97%  387 MB
|=====================================================================================================================================================    |  97%  388 MB
|=====================================================================================================================================================    |  97%  388 MB
|======================================================================================================================================================   |  97%  388 MB
|======================================================================================================================================================   |  97%  389 MB
|======================================================================================================================================================   |  97%  389 MB
|======================================================================================================================================================   |  97%  389 MB
|======================================================================================================================================================   |  97%  390 MB
|======================================================================================================================================================   |  97%  390 MB
|======================================================================================================================================================   |  97%  390 MB
|======================================================================================================================================================   |  98%  391 MB
|=======================================================================================================================================================  |  98%  391 MB
|=======================================================================================================================================================  |  98%  391 MB
|=======================================================================================================================================================  |  98%  392 MB
|=======================================================================================================================================================  |  98%  392 MB
|=======================================================================================================================================================  |  98%  392 MB
|=======================================================================================================================================================  |  98%  393 MB
|=======================================================================================================================================================  |  98%  393 MB
|======================================================================================================================================================== |  98%  393 MB
|======================================================================================================================================================== |  98%  394 MB
|======================================================================================================================================================== |  98%  394 MB
|======================================================================================================================================================== |  98%  394 MB
|======================================================================================================================================================== |  99%  395 MB
|======================================================================================================================================================== |  99%  395 MB
|======================================================================================================================================================== |  99%  395 MB
|======================================================================================================================================================== |  99%  396 MB
|=========================================================================================================================================================|  99%  396 MB
|=========================================================================================================================================================|  99%  396 MB
|=========================================================================================================================================================|  99%  397 MB
|=========================================================================================================================================================|  99%  397 MB
|=========================================================================================================================================================|  99%  397 MB
|=========================================================================================================================================================|  99%  398 MB
|=========================================================================================================================================================|  99%  398 MB
|=========================================================================================================================================================|  99%  398 MB
|==========================================================================================================================================================| 100%  398 MB
snps

filter to keep snps where there is data from all samples

snps <- snps %>% 
  filter({select(., matches("[0-9]")) %>% complete.cases() })
snps
snps <- snps %>% 
  filter(QUAL >=50,
         nchar(ALT)==1)
snps
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